The sequencing of whole genomes is producing information at an unprecedented pace. This information is accelerating, and in some cases changing, the goals of the molecular biologist. Most current genomic analysis is focused on identifying genes and comparing their encoded proteins. While the analysis of proteins is essential for understanding human biology, protein-coding sequences account for only a small portion of the human genome. Other important genomic features, such as promoter regulatory elements and non-coding RNAs, need to be identified and characterized as they also contribute to diseases. Many of these sequence features are hard to identify because they are short or they evolve more quickly than protein-coding sequences. Comparative sequence analysis will be employed to identify important parts of the yeast genome that are conserved between related species. The work utilizes large-scale sequencing of genomes of different yeast species followed by comparisons to identify the conserved features. The hypothesis generated by these computational methods will then be tested experimentally to determine their biological significance. The lesson learned and experience gained in this analysis of the yeast genome will help guide future characterizations of the human genome.